Updates

Model and report changes

  1. The model incorporates estimates of community prevalence, by region and age group, from the Office of National Statistics COVID-19 Infection Survey (see Data Sources for details). These are included weekly over the last 50 days and for the age groups >4 years to inform trends in incidence that are too recent to be captured by the data on deaths.
  2. The geographical definition has been changed from the seven NHS regions (map) to the nine regions typically used in government (map). This new spatial definition more appropriately reflects the existing regional heterogeneity.
  3. Using observations of improved survival in hospitalised COVID-19 patients, we have allowed the probability of dying following infection with SARS-CoV2 (the infection-fatality rate, IFR) to gradually change over the course of June 2020, with a decrease being estimated.
  4. The modelling now accounts for a different susceptibility to infection in the under-15s, using information from literature (Viner et al, 2020) suggesting that children less likely to acquire infection when in contact with an infectious individual.

Updated findings

  1. The current estimate of the daily number of new infections occurring each day across England is 86,000 (60,300–124,000, 95% credible interval).
  2. The daily infection rate is particularly high in the North West (NW) and North East (NE) with 22,800, 6,160 new daily infections, corresponding to 313, and 232 per 100,000 population, respectively. Note that a substantial proportion of these daily infections will be asymptomatic.
  3. We predict that the number of deaths occurring daily is likely to be between 550 and 1040 on the 10th February 2021.
  4. The probability of Rt exceeding 1 is 83% and 79% in the NW and South West (SW) respectively; 69% in NE; 55% in Yorkshire and Humber (YH); 30% in the East Midlands (EM); 26% in the West Midlands (WM) and lower than 10% in London, the South East (SE) and East of England (EE).
  5. The growth rate for England is now estimated to be 0.01 (-0.02–0.03, 95% credible interval) per day. This means that, nationally, the number of infections is slightly increasing, but with a high degree of regional variation. Infections are still increasing in the SW, NE and NW, plateauing in YH, and decreasing in all other regions.
  6. London, followed by the NW, the NE and WM, continues to have the highest attack rate, that is the proportion of the population who have ever been infected, with 37%, 33% and 27% respectively. The SW continues to have the lowest attack rate at 11%.
  7. Note that the deaths data used are only very weakly informative on Rt over the last two weeks. Therefore, the estimate for current incidence, Rt and the forecast of daily numbers of deaths are likely to be subject to some revision.

Interpretation

The plots of Rt over time are showing a plateau in the estimated values, following a period of downwards trends from the introduction of the national Tier 4 restrictions and the beginning of the Christmas period. Many of the Rt values are below 1, notably in London, the EE and the SE, but remain higher than 1 in the SW, NW, NE and YH where the number of infections is increasing (SW, NW, NE) or plateauing (YH).

Incidence of deaths which had levelled off during the last week of November / first week of December, with some falls noted in the NE, NW, and YH, EM and WM started to climb significantly throughout December and early January in all regions. The deaths, which are now at a level similar to (e.g. London and WM) or higher than the first wave (SE and EE) are predicted to start falling in most regions, with the exception of regions where the number of new infections is still growing (SW, NW, NE).

In most regions, a downward trend in Rt started around the time of the launch of Tier 4 restrictions on Saturday 19th December appears to have been consolidated by the Christmas holiday period and the nationwide lockdown announced on the 5th January. It is difficult to separate the individual impacts of each, though in four regions (EE, London, SE and WM), the sharpest drop coincides with the timing of this latest lockdown, whereas in the Northern regions (NE, NW, YH) there is no appreciable decline in Rt after an initial drop when schools first closed over the Christmas period. In these regions Rt remains above 1.

However, due to the recency of the lockdown, its estimated impact is highly volatile and, with a high likelihood, could change over the coming week. This, combined with the conflicting signals from the two primary data streams (over a number of weeks the deaths continue to increase while prevalence declines), gives a reduced confidence in our outputs this week. Other indicators (e.g. hospital bed prevalence, case data etc) currently suggest a declining epidemic, so an estimate of positive epidemic growth may be a little unreliable. Conversely, it is this data conflict that leads to a very low estimate for Rt in EE, which should be treated with caution. Regardless of current trends, the prevalence of infection remains high and the demand on healthcare services is currently extreme, so continued restrictions are essential to lower these levels and to gain control over transmission over the coming period.

Summary

Real-time tracking of an epidemic, as data accumulate over time, is an essential component of a public health response to a new outbreak. A team of statistical modellers at the MRC Biostatistics Unit (BSU), University of Cambridge, are working to provide regular now-casts and forecasts of COVID-19 infections and deaths. This information feeds directly to the SAGE sub-group, Scientific Pandemic Influenza sub-group on Modelling (SPI-M), and to regional Public Health England (PHE) teams.

Methods

We fit a transmission model (Birrell et al. 2020) to a number of data sources (see ‘Data Sources’), to reconstruct the number of new COVID-19 infections over time in different age groups and NHS regions, estimate a measure of ongoing transmission and predict the number of new COVID-19 deaths.

Data sources

We use:

  1. Data on COVID-19 confirmed deaths from the Public Health England (PHE) line-listing. The definition of a COVID-19 confirmed death is any death that occurs in an individual who had a lab-confirmed infection, within 60 days from the date of their most recent positive test. This definition reflects more realistically the burden of COVID-19. This consists of a combination of deaths notified to:
    • the Demographics Batch Service (DBS), a mechanism that allows PHE to submit a file of patient information to the National Health Service spine for tracing against the personal demographics service (PDS). PHE submit a line list of patients diagnosed with COVID-19 to DBS daily. The file is returned with a death flag and date of death updated (started 20th March, 2020).
    • NHS England, who report data from NHS trusts relating to patients who have died after admission to hospital or within emergency department settings.
    • Health Protection Teams (HPTs), resulting from a select survey created by PHE to capture deaths occurring outside of hospital settings, e.g. care homes (started 23rd March, 2020).
  2. Data on antibody prevalence in blood samples from a PHE survey of NHS Blood Transfusion (NHSBT) donors. From early June, the NHSBT began giving a constantly declining prevalence of antibodies, making them no longer an accurate measure of cumulative infection. Consequently, these data have been curtailed at this time.
  3. Age- and region-specific estimates of community prevalence of PCR positive COVID-19 infection as derived from the COVID-19 Infection Survey of the Office for National Statistics (ONS) using the methodology of Pouwels et al., 2020.

Data are stratified into eight age groups: <1, 1-4, 5-14, 15-24, 25-44, 45-64, 65-74, 75+, and the NHS England regions (North East and Yorkshire, North West, Midlands, East of England, London, South East, South West).

  1. Published information on the the natural history of COVID-19 (Verity et al., 2020; Li et al, 2020)
  2. Information on contacts between different age groups from:
    • A Survey that describes relative rates of contacts between different age groups (Mossong et al. 2008).
    • Google Community Mobility reports, informing the changes in people’s mobility over the course of the pandemic, particularly after the March 23rd lockdown measures.
    • The ONS’ time use survey, which in conjunction with the google mobility study, allows estimation of the changing exposure to infection risk over time.
    • Data from the Department for Education describing the proportion of children currently attending school.

Epidemic summary

Current \(R_t\)

Value of \(R_t\), the average number of secondary infections due to a typical infection today.

Number of infections

Attack rate

The percentage of a given group that has been infected.

By region

By age

IFR

Change in infections incidence

Growth rates

NB: negative growth rates are rates of decline. Values are daily changes.

Region Median 95% CrI (lower) 95% CrI (upper)
England 0.01 -0.02 0.03
East of England -0.10 -0.15 -0.05
East Midlands -0.01 -0.06 0.04
London -0.05 -0.10 0.00
North East 0.02 -0.04 0.07
North West 0.02 -0.03 0.06
South East -0.04 -0.09 0.01
South West 0.03 -0.03 0.08
West Midlands -0.02 -0.07 0.04
Yorkshire and The Humber 0.01 -0.05 0.06

Halving times

Halving times in days, if a region shows growth than value will be NA.

Region Median 95% CrI (lower) 95% CrI (upper)
England NA 42.57 NA
East of England 6.54 4.29 13.28
East Midlands 70.83 10.80 NA
London 13.70 6.67 328.02
North East NA 19.22 NA
North West NA 25.92 NA
South East 15.80 7.07 NA
South West NA 22.41 NA
West Midlands 45.02 10.07 NA
Yorkshire and The Humber NA 13.93 NA

Doubling times

Doubling times in days, if a region shows decline then the value will be NA.

Region Median 95% CrI (lower) 95% CrI (upper)
England 107.88 21.50 NA
East of England NA NA NA
East Midlands NA 17.14 NA
London NA NA NA
North East 41.28 10.60 NA
North West 30.32 10.81 NA
South East NA 59.36 NA
South West 24.94 8.60 NA
West Midlands NA 19.56 NA
Yorkshire and The Humber 114.39 11.17 NA

Change in deaths incidence

Growth rates

NB: negative growth rates are rates of decline. Values are daily changes.

Region Median 95% CrI (lower) 95% CrI (upper)
England -0.02 -0.03 -0.01
East of England -0.05 -0.06 -0.04
East Midlands -0.02 -0.04 0.01
London -0.04 -0.05 -0.02
North East 0.00 -0.03 0.04
North West 0.01 -0.02 0.04
South East -0.03 -0.05 -0.01
South West 0.01 -0.02 0.05
West Midlands -0.02 -0.04 0.01
Yorkshire and The Humber -0.01 -0.04 0.02

Halving times

Halving times in days, if a region shows growth than value will be NA.

Region Median 95% CrI (lower) 95% CrI (upper)
England 39.29 26.70 96.24
East of England 12.56 11.02 16.00
East Midlands 41.41 18.90 NA
London 18.73 13.71 44.03
North East NA 26.96 NA
North West NA 36.23 NA
South East 19.86 14.14 63.06
South West NA 34.13 NA
West Midlands 39.22 18.42 NA
Yorkshire and The Humber 56.41 19.42 NA

Doubling times

Doubling times in days, if a region shows decline then the value will be NA.

Region Median 95% CrI (lower) 95% CrI (upper)
England NA NA NA
East of England NA NA NA
East Midlands NA 51.29 NA
London NA NA NA
North East 805.87 17.41 NA
North West 89.91 15.67 NA
South East NA NA NA
South West 73.23 14.16 NA
West Midlands NA 52.97 NA
Yorkshire and The Humber NA 29.79 NA

Infections and deaths

The blue lines is show when interventions have been introduced (lockdown on 23 Mar and the relaxation of measures on 11 May), and the red line shows the date these results were produced (25 Jan).

Infection incidence

By region

By age

Cumulative infections

By region

By age

Deaths incidence

By region

By age

Cumulative deaths

By region

By age

Prob \(R_t > 1\)

The figure below shows the probability that \(R_t\) is greater than 1 (ie: the number of infections is growing) in each region over time. Clicking the regions in the legend allows lines to be added or removed from the figure.

\(R_t\)

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